Chemistry Commons^™

Tcr Scanning Of Peptide/Mhc Through Complementary Matching Of Receptor And Ligand Molecular Flexibility, William F. Hawse, Soumya De, Alexander I. Greenwood, Linda K. Nicholson, Jaroslav Zajicek, Evgeni L. Kovrigin, David M. Kranz, K. Chrisopher Garcia, Brian M. Baker

Chemistry Faculty Research and Publications

Although conformational changes in TCRs and peptide Ags presented by MHC protein (pMHC) molecules often occur upon binding, their relationship to intrinsic flexibility and role in ligand selectivity are poorly understood. In this study, we used nuclear magnetic resonance to study TCR–pMHC binding, examining recognition of the QL9/H-2L^d complex by the 2C TCR. Although the majority of the CDR loops of the 2C TCR rigidify upon binding, the CDR3β loop remains mobile within the TCR–pMHC interface. Remarkably, the region of the QL9 peptide that interfaces with CDR3β is also mobile in the free pMHC and in the TCR–pMHC complex. …

Spectroscopic Studies Of Conformation And Packing In Polythiophenes, Edwards T. Niles

Chemistry and Chemical Biology ETDs

This thesis employs variants of spectroscopic techniques to evaluate intermolecular interactions between P3HT chains in solution and in the solid state. Emphasis was put on understanding not only how intermolecular interactions within P3HT chains affect electronic properties, but also to assess changes due to the addition of weak and strong electron acceptors. To this end, optical and magnetic spectroscopies were focused on to correlate observed changes in electronic properties to physical changes in the polymer structure. To assess changes in intermolecular interactions, self-assembly was used to form P3HT nanofibers and were studied using resonance Raman, and transient absorption, and temperature- …

Effects Of Statin Drugs And Tocotrienol Rich Fraction Supplementation In Chronic Hemodialysis Patients And Metabolomic Profile, Eno Latifi

Wayne State University Theses

Chronic kidney disease (CKD) is known as a heterogeneous disorder which currently is on the rise and lately has been classified as a public health issues in the United State and worldwide. CKD is an irreversible and progressive disease which can lead to kidney failure, and this is depicted by the advanced stage of the disorder when it reaches the point, that is classified as end stage of renal disease (ESRD) (Stage 5 of CKD) (eGRF <15 mL/min/ 1.73 m2 working capacity), where both organs are in a total or permanent kidney failure. End-Stage renal disease patients, on hemodialysis have been associated to experience an accelerated form of atherosclerosis, which is induced by inflammation, impairment of antioxidant system and elevated oxidative stress. Since the problem effecting ESRD patients is multifactorial, the objective of this investigation is to explore and look at the effects of supplementing with vitamin E-tocotrienol rich fraction (TRF), a micronutrient which has anti-inflammatory, antioxidant, and lipid lower capabilities into tackling these comorbid conditions experienced by this population. Therefore the aims of this investigation will be to explore changes in lipid profiles, inflammatory markers, and oxidative status, as well as look at any changes in metabolomic profiles. It was hypothesized that by supplementing with TRF a vitamin E, for 16 weeks in ESRD patients undergoing hemodialysis, it may help reverse and/or improve, oxidative status, inflammatory markers, increase antioxidants status and improve lipid profiles.

The study was double-blinded, randomized, parallel, placebo-controlled design trial, of 81 adult patients undergoing chronic hemodialysis at Great Lake Dialysis Clinic, Detroit MI, where …

Structure And Function Of Preq1 Riboswitches, Catherine D. Eichhorn, Mijeong Kang, Juli Feigon

Department of Chemistry: Faculty Publications

PreQ₁ riboswitches help regulate the biosynthesis and transport of PreQ₁ (7-aminomethyl-7- deazaguanine), a precursor of the hypermodified guanine nucleotide queuosine (Q), in a number of Firmicutes, Proteobacteria, and Fusobacteria. Queuosine is almost universally found at the wobble position of the anticodon in asparaginyl, tyrosyl, histidyl and aspartyl tRNAs, where it contributes to translational fidelity. Two classes of PreQ₁ riboswitches have been identified (PreQ₁-I and PreQ₁-II), and structures of examples from both classes have been determined. Both classes form H-type pseudoknots upon PreQ₁ binding, each of which has distinct unusual features and modes …

Spectroscopic Characterization Of Dissolved Organic Matter: Insights Into The Linkage Between Sources And Chemical Composition, Xiaoyan Cao

Chemistry & Biochemistry Theses & Dissertations

This dissertation investigated the chemical structure of DOM by advanced solid-state nuclear magnetic resonance (NMR) spectroscopy and Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) techniques, as well as isotopic measurements and UV-visible spectroscopy, to shed light on the linkages between DOM sources and DOM composition. Unique and extensive sets of DOM samples studied here were isolated from various aquatic systems, covering end-member environments in which DOM is considered either microbially derived or terrestrially derived, and areas in which DOM has characteristics intermediate between the two end members. Important insights into specific site-related questions were also gained such as …

Synthesis, Structural Variations And Trends In The Properties Of Unique Dinuclear And Polynuclear Complexes Of Bis(Pyrazolyl)Methane Ligands In Solid State And Solution, Andrea Eva Pascui

Theses and Dissertations

The semi-rigid ligands, p-[CH(pz)₂]₂C₆H₄, L_p, m-[CH(pz)₂]₂C₆H₂, L_m, and m-[CH(3,5-Me₂pz)₂]₂C₆H₄, L_m* (pz = pyrazolyl ring), link two bis(pyrazolyl)methane units into a single molecule by a rigid phenylene spacer and are used to study the structural variations and magnetic interactions in self-assembled first row, divalent transition metal complexes in polymeric, dinuclear and dinuclear metallacyclic settings. The formation of these architectures highly depend on the geometry of these ligands: anti, the …

The Development And Applications Of Nmr Metabolomics Analysis Of Bacterial Metabolomes, Steven M. Halouska

Department of Chemistry: Dissertations, Theses, and Student Research

Metabolomics is a relatively new field that involves the study of metabolic responses that are occurring within a biological system. Metabolite profiles of an organism, tissue extract, and biofluids are important indicators to determine the physiological state of a biological profile. Comparison of such profiles from different phenotypes can be used to identify specific metabolic changes leading to the understanding of metabolic pathways, disease progression, drug toxicity and efficacy, and cellular responses to different intracellular and extracellular conditions. Metabolomics investigations often use sophisticated analytical techniques such as NMR spectroscopy to provide an unbiased and comprehensive approach to evaluate metabolic perturbation …

Investigate And Study Of The Properties Of 2,2-Dipicolyamine And It Interactions With Anions, Martin Conda Sheridan, Dr. John Lamb

Journal of Undergraduate Research

Compared to cation ligand interactions, anion ligand studies are less well known. We studied the interactions of protonated cavitands, Fig 1, with anions because of their many applications, including: environmental waste remediation, anion separation, binding constant determination, and molecular structure recognition.

Englerin-A, Curtis Allred, Dr. Merritt Andrus

Journal of Undergraduate Research

My project has been to synthesize smaller, simpler analogs of a molecule that is effective against renal cancer, called englerin-A.

Solution Structures Of Mycobacterium Tuberculosis Thioredoxin C And Models Of Intact Thioredoxin System Suggest New Approaches To Inhibitor And Drug Design, Andrew Lawrence Olson, Terrence S. Neumann, Sheng Cai, Daniel S. Sem

Chemistry Faculty Research and Publications

Here, we report the NMR solution structures of Mycobacterium tuberculosis (M. tuberculosis) thioredoxin C in both oxidized and reduced states, with discussion of structural changes that occur in going between redox states. The NMR solution structure of the oxidized TrxC corresponds closely to that of the crystal structure, except in the C-terminal region. It appears that crystal packing effects have caused an artifactual shift in the α4 helix in the previously reported crystal structure, compared with the solution structure. On the basis of these TrxC structures, chemical shift mapping, a previously reported crystal structure of the M. tuberculosis …

Utilizing Nmr Spectroscopy And Molecular Docking As Tools For The Structural Determination And Functional Annotation Of Proteins, Jaime Stark

Department of Chemistry: Dissertations, Theses, and Student Research

With the completion of the Human Genome Project in 2001 and the subsequent explosion of organisms with sequenced genomes, we are now aware of nearly 28 million proteins. Determining the role of each of these proteins is essential to our understanding of biology and the development of medical advances. Unfortunately, the experimental approaches to determine protein function are too slow to investigate every protein. Bioinformatics approaches, such as sequence and structure homology, have helped to annotate the functions of many similar proteins. However, despite these computational approaches, approximately 40% of proteins still have no known function. Alleviating this deficit will …

Oligomers Of Beta-L-Arabinosides Of Hydroxyproline : Synthesis Of The Carbohydrate Epitope Of The Art V 1 Allergen, Ning Xie

LSU Doctoral Dissertations

The pollen of mugwort is a major contributor to hay fever in Europe and North America. The chemical structure of Art v 1, the major allergen of mugwort, has been elucidated. A notable motif in Art v 1 – characterized by clusters of contiguous â-arabinosides of hydroxyproline – was found to be a key recognition element for antibodies generated in response to the natural protein. This dissertation details the chemical synthesis of oligomers of â-arabinosides of hydroxyproline and the search to establish the minimal carbohydrate epitope of Art v 1. The â-arabinoside motif, being a 1,2-cis glycoside, presents a considerable …

Investigations Into Alkene Hydration And Alkene Oxidation Catalysis, William Schreiter

LSU Doctoral Dissertations

Bimetallic Ni complexes Ni21M and Ni21R and monometallic transition metal complexes were investigated as possible alkene hydration catalysts under a multitude of different reaction conditions. All attempts at performing this catalytic reaction failed to give any alcohol products. Catalytic screening experiments were conducted using a mixture of racemic-et,ph-P4 and meso-et,ph-P4, 1M and 1R, and various transition metals. These experiments gave several different products including 1-phenylethanol from styrene. During the course of the hydration experiments, an aldehyde product was identified from experiments conducted with the bimetallic complexes in air. Experiments have shown that the aldehyde is produced from the oxidative cleavage …

Experimental And Theoretical Studies In Nuclear Magnetic Resonance, John D. Persons

Department of Chemistry: Dissertations, Theses, and Student Research

Nuclear Magnetic Resonance (NMR) has proven to be an excellent tool to probe the structure of molecules by gaining insight into nuclear interactions. Used in conjunction with theoretical calculations, NMR has the potential to elucidate these nuclear interactions and how they affect structure, bonding and dynamics on a molecular scale. The first two projects presented herein study the peroxide explosive hexamethylene triperoxide diamine (HMTD). In the first project, we use the characteristics of the solid-state NMR lineshape to determine the ¹⁴N quadrupole coupling constant (C_Q). The second project uses multi-dimensional solution-state NMR and chiral shift reagents …

Experimental And Theoretical Studies In Solid-State Nuclear Magnetic Resonance, Monica N. Kinde

Department of Chemistry: Dissertations, Theses, and Student Research

Solid-state nuclear magnetic resonance (SSNMR) has proven to be a powerful tool for probing molecular structure and dynamics. Deuterium SSNMR is particularly useful due to the presence of anisotropic interactions whose motional averaging contributes structural and dynamical insight. The magnitude and type of molecular motion can be determined from analysis of solid echo deuterium lineshapes and/or relaxation studies. This work uses various applications of solid-state NMR as well as ab initio and density functional computational methods to study three different areas of physical chemistry: biophysical chemistry, materials science and fundamental concepts of physical chemistry. The first project addressed the dynamics …

Design And Synthesis Of Protein-Protein Interaction Inhibitor Scaffolds, David B. Badger

USF Tampa Graduate Theses and Dissertations

Many currently relevant diseases such as cancer arise from altered biological pathways that rely on protein-protein interactions. The proteins involved in these interactions contain certain functional domains that are responsible for the protein's biological activities. These domains consist of secondary structural elements such as α-helices and Β-sheets which are at the heart of the protein's biological activity. Therefore, designing drugs that inhibit protein-protein interactions by binding to these key secondary structural elements should provide an effective treatment for many diseases. Presented in this dissertation are the designs, syntheses, and biological evaluations for both novel α-helix and novel Β-sheet mimics.

The …

Nmr Line Shapes And Multi-State Binding Equilibria, Evgenii L. Kovrigin

Chemistry Faculty Research and Publications

Biological function of proteins relies on conformational transitions and binding of specific ligands. Protein-ligand interactions are thermodynamically and kinetically coupled to conformational changes in protein structures as conceptualized by the models of pre-existing equilibria and induced fit. NMR spectroscopy is particularly sensitive to complex ligand-binding modes—NMR line-shape analysis can provide for thermodynamic and kinetic constants of ligand-binding equilibria with the site-specific resolution. However, broad use of line shape analysis is hampered by complexity of NMR line shapes in multi-state systems. To facilitate interpretation of such spectral patterns, I computationally explored systems where isomerization or dimerization of a protein (receptor) molecule …

Structural Interactions And Dynamics Of Disease Related Proteins By Using Nmr Spectroscopy, Shadakshara Swamy Puttamadappa

Legacy Theses & Dissertations (2009 - 2024)

Nuclear Magnetic Resonance (NMR) is a powerful spectroscopic technique to study the structure, molecular interactions, and dynamics of proteins. Modern NMR instrumentation, advancements in experimental techniques and revolutionary developments in recombinant DNA technology have made NMR a versatile and very convenient tool for biomolecule characterization.

In-Cell And In Vitro Studies Of Disease Related Protein-Protein Interactions Using Nmr-Spectroscopy, Andres Yudiel Maldonado

Legacy Theses & Dissertations (2009 - 2024)

The receptor for advanced glycation end products (RAGE) is a multiligand cell surface macromolecule that plays a central role in the etiology of diabetes, inflammation, and neurodegeneration. The cytoplasmic domain of RAGE, ctRAGE, is critical for RAGE-dependent signal transduction. As the most membrane proximal event, mDia1 binds to ctRAGE and is essential for RAGE ligand-stimulated phosphorylation of AKT and cell proliferation/migration. We show that ctRAGE contains an unusual alpha-turn that mediates the mDia1-ctRAGE interaction and is required for RAGE dependent signaling. The results establish a novel mechanism through which an extracellular signal initiated by RAGE ligands regulates RAGE signaling in …

Homologous And Heterologous Crystallin Protein Interactions As The Molecular Basis Of Inherited Cataract, Priya Ranjan Banerjee

Legacy Theses & Dissertations (2009 - 2024)

Age-related cataract is the most common cause of blindness worldwide. Nearly fifty percent of Americans above the age of 75 are diagnosed with this disease (http://www.nei.nih.gov/eyedata/pbd_tables.asp), and surgical intervention is the sole method of treatment at present (http://www.nei.nih.gov/healthyvision/objective/cataracts.asp). In the developing world, even this treatment is not readily available. These are compelling reasons to search for better treatments to delay, prevent or arrest cataract formation. Recent evidence suggests that age-related cataracts also have a genetic component. Therefore, determining the mechanisms underlying genetic cataracts with a known association to a protein-mutation is one important strategy towards understanding the molecular basis for …

Nuclear Magnetic Resonance Affinity Screening Methods For Functional Annotation Of Proteins And Drug Discovery, Matthew D. Shortridge

Department of Chemistry: Dissertations, Theses, and Student Research

With nearly 1,350 complete genome sequences available our understanding of biology at the molecular level has never been more complete. A consequence of these sequencing projects was the discovery of large functionally unannotated segments of each genome. The genes (and proteins they encode) found in these unannotated regions are considered “hypothetical proteins”. Current estimates suggest between 12%-50% of the known gene sequences are functionally unannotated. Incomplete functional annotation of the various genomes significantly limits our understanding of biology. Pragmatically, identifying the functions of these proteins could lead to new therapeutics; making functional annotation of paramount importance.

This dissertation describes the …

A Synthetic Biological Engineering Approach To Secretion- Based Recovery Of Polyhydroxyalkanoates And Other Cellular Products, Elisabeth Linton

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

The costs associated with cellular product recovery commonly account for as much as 80% of the total production expense. As a specific example, significant recovery costs limit commercial use of polyhydroxyalkanoates (PHA), which comprise a class of microbially-accumulated polyesters. PHAs are biodegradable compounds that are of interest as a sustainable alternative to petrochemically-derived plastics. Secretion-based recovery of PHAs was studied to decrease PHA production costs. Type I and II secretory pathways are commonly used for the translocation of recombinant proteins out of the cytoplasm of E. coli. Proteins were targeted for translocation using four signal peptides (HlyA, TorA, GeneIII, …

Identification And Quantitation Of 3,4-Methylenedioxy-N-Methylamphetamine (Mdma, Ecstasy) In Human Urine By 1h Nmr Spectroscopy. Application To Five Cases Of Intoxication, Jonathan Liu, John Decatur, Gloria Proni, Elise Champeil

Publications and Research

Identification of 3,4-methylenedioxy-N-methylamphetamine (MDMA, ecstasy) in five cases of intoxication using nuclear magnetic resonance (NMR) spectroscopy of human urine is reported. A new water suppression technique PURGE (Presaturation Utilizing Relaxation Gradients and Echoes) was used. A calibration curve was obtained using spiked samples. The method gave a linear response (correlation coefficient of 0.992) over the range 0.01–1 mg/mL. Subsequently, quantitation of the amount of MDMA present in the samples was performed. The benefit and reliability of NMR investigations of human urine for cases of intoxication with MDMA are discussed.

Effect Of Various Substituents On Intramolecular 1,1-Vinylboration, Synthesis Of 1-Silacyclobutene Derivatives, Ezzat Khan, Bernd Wrackmeyer

Turkish Journal of Chemistry

The reaction of 1-boryl-1-alkenyl chlorosilane derivatives with alkynyllithium reagents [Li-C\equiv C-R^3 (R^3~=~Ph, SiMe_3)] at low temperature (--78 °C) affords alkenyl(alkyn-1-yl)silanes. These compounds are precursors of 1-silacyclobutene derivatives, which are formed via intramolecular 1,1-vinylboration. This reaction works for various groups at silicon (R^1/R^2: R^1 = H, Me, Ph; R^2 = Me, Ph) and at the C=C and C\equiv C units (R/R^3: R = ^nBu, Ph; R^3 = ^nBu, Ph, SiMe_3). The conversion into 1-silacyclobutene derivatives is incomplete only in the case of R^3 = SiMe_3. The reactions were monitored by NMR spectroscopy in order to elucidate the reaction mechanism, and the …

Isolation And Identification Of A New Acetildenafil Analogue Used To Adulterate A Dietary Supplement: Dimethylacetildenafil, Ali̇ Hakan Göker, Maksut Coşkun, Mehmet Alp

Turkish Journal of Chemistry

A new sildenafil analogue was found to have been added illegally to a dietary supplement marketed for the enhancement of sexual function. The structure was determined as 5-(2-ethoxy-5- {[4-(3,5-dimethyl)piperazin-1-yl]-acetyl}phenyl)-1,6-dihydro-1-methyl-3- propyl-7H-pyrazolo [4,3-d]pyrimidin-7-one. Owing to the inclusion of a dimethyl group in acetildenafil, the detected compound was called dimethylacetildenafil. The sample was purified with column chromatography. The IR, LC/MS (ESI), and completely assigned NMR data of dimethylacetildenafil are reported for the first time. The structure was compared with that of acetildenafil and the results showed that the ethyl substitution at the 4-position of the piperazine ring had been replaced by a 3,5-dimethyl …

Small Molecule Caspase Inhibitors Using Isatin And Oxindole Scaffolds And A Combinatorial Approach, Hagar Mahmoud Abdallah

Browse all Theses and Dissertations

Quinolyl-valyl-O-methylaspartyl-[2,6-difluorophenoxy]-methyl ketone (Q-VD-OPh) is a next generation broad spectrum caspase inhibitor, the effectiveness and reduced toxicity of which can be partially attributable to the carboxyterminal O-phenoxy group as well as the amino terminal quinolyl groups. We seek to incorporate some of these unique recognition elements onto small molecule derived protease inhibitors with drug like properties. Specifically, heterocyclic scaffolds such as isatins and oxindoles. Thus, isatins bearing electron withdrawing groups on C-5 and 2,6-difluorobenzyl moieties have been prepared by analogy to the well studied N-substituted 5-pyrrololidinylsulfonyl isatins. Moreover, 3-benzylidene oxindole derivatives bearing these structural motifs have also been prepared and their …

The Separation And Indentification Of Polyoxometalate Mixtures, Stephanie Peterson

Honors Capstones

Capstone submitted as a graduate requirement for the BSU Honors Program.

Structural Investigation Of The Complex Of Filamin A Repeat 21 With Integrin Αiib And Β3 Cytoplasmic Tails – A Potential “Transmission” To Regulate Cell Migration, Jianmin Liu

ETD Archive

Cell functions in multi-cellular organisms are strongly depend on the dynamic cooperation between cell adhesion and cytoskeleton reorganization. Integrins, the major cell adhesion receptors, bind to extracellular matrix (ECM) and soluble ligands on the cell surface and link to the actin cytoskeleton inside the cell membrane. In this manner, integrins integrate cell adhesion and cytoskeleton reorganization by acting as a mechanical force transducer and a biochemical signaling hub (Zamir and Geiger 2001). Consequently, integrins are vital for development, immune responses, leukocyte traffic and hemostasis, and a variety of other cellular and physiological processes. Integrins are also are the focal point …

Cationic Exchange Reactions Involving Dilithium Phthalocyanine, Morgan M. Hart

Browse all Theses and Dissertations

Dilithium phthalocyanine (Li₂Pc) consists of an aromatic macrocycle possessing a doubly negative charge and two Li⁺ counterions. One Li⁺ ion is easily displaceable while the other remains coordinated to the phthalocyanine ring. The displaceable Li⁺ cation can be exchanged with other cations, such as a singly charged tetra-alkyl ammonium cation, by using several variations of a general procedure. It has been demonstrated that tetraalkylammonium lithium phthalocyanines (TAA-LiPcs) can be successfully and reproducibly synthesized with yields ranging from 54.5% up to 64.3%. All TAA-LiPcs demonstrated poor solubilities from approximately <0.2 mg/mL to 5 mg/ml in the solvents tested (with the exception of tetrapropylammonium lithium phthalocyanine and tetrahexylammonium lithium phthalocyanine). All of the TAA-LiPcs synthesized were dark-purple in color, with the exception of tetraheptylammonium lithium phthalocyanine and tetraoctylammonium lithium phthalocyanine. These two compounds were dark - blue in color. Melting points varied greatly from >370.4°C to 157.9°C and depended greatly upon …

Substrate Induced Structural And Dynamics Changes In Human Phosphomevalonate Iinase And Implications For Mechanism, Andrew Lawrence Olson, Huili Yao, Timothy J. Herdendorf, Henry M. Miziorko, Supa Hannongbua, Patchareenat Saparpakom, Sheng Cai, Daniel S. Sem

Chemistry Faculty Research and Publications

Phosphomevalonate kinase (PMK) catalyzes an essential step in the mevalonate pathway, which is the only pathway for synthesis of isoprenoids and steroids in humans. PMK catalyzes transfer of the γ-phosphate of ATP to mevalonate 5-phosphate (M5P) to form mevalonate 5-diphosphate. Bringing these phosphate groups in proximity to react is especially challenging, given the high negative charge density on the four phosphate groups in the active site. As such, conformational and dynamics changes needed to form the Michaelis complex are of mechanistic interest. Herein, we report the characterization of substrate induced changes (Mg-ADP, M5P, and the ternary complex) in PMK using …